junctionCount: Count junctions

In LieberInstitute/jaffelab: Commonly used functions by the Jaffe lab

Count junctions

Description

Count junctions from either TopHat2, HISAT2 or Rail-RNA output

Usage

junctionCount(
  junctionFiles,
  sampleNames = names(junctionFiles),
  output = c("Count", "Rail"),
  minOverhang = 0,
  strandSpecific = FALSE,
  illuminaStranded = FALSE,
  minCount = 1,
  maxCores = 1,
  skipLines = ifelse(output == "Count", 0, 1)
)

Arguments

junctionFiles	A character vector with the full paths to the junction files. Can alternatively be a list of GRanges-class objects with the junction count information.
sampleNames	A character vector of the same length as junctionsFiles to use as the sample names.
output	Either Count (TopHat2, HISAT2) or Rail (Rail-RNA).
minOverhang	minimum overhang.
strandSpecific	a logical specifying whether the library is strand specific or not.
illuminaStranded	a logical indicating whether the Illumina library is stranded or not.
minCount	Minimum count.
maxCores	The maximum number of cores to use. By default one.
skipLines	An integer(1) specifying how many lines to skip on the junction files. Some files have a header and some don't. So you'll either want to use 1 or 0 in most scenarios.

Value

A two element list with a DataFrame and a GRanges-class object with the counts and the annotation used.

Author(s)

Andrew E Jaffe

Examples

## TODO (need some data)
## See https://github.com/LieberInstitute/RNAseq-pipeline/blob/ab71dedb36bcc3dad57233e645fabd5deb96d446/sh/create_count_objects-human.R#L633-L643
## for an example of how it's being using the the RNA-seq pipeline code

LieberInstitute/jaffelab documentation built on April 1, 2024, 7:26 a.m.